{ "type": "genome", "identifier": "GCF_010728725.1", "organism": "Mycobacterium branderi", "title": "Mycobacterium branderi", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Department of Infection Metagenomics, Osaka University", "publication": [ {} ], "properties": { "assembly_accession": "GCF_010728725.1", "bioproject": "PRJNA224116", "biosample": "SAMD00153181", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "43348", "species_taxid": "43348", "organism_name": "Mycobacterium branderi", "infraspecific_name": "strain=JCM 12687", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2020/02/06", "asm_name": "ASM1072872v1", "asm_submitter": "Department of Infection Metagenomics, Osaka University", "gbrs_paired_asm": "GCA_010728725.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/010/728/725/GCF_010728725.1_ASM1072872v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "5979623", "genome_size_ungapped": "5979623", "gc_percent": "66.500000", "replicon_count": "2", "scaffold_count": "2", "contig_count": "2", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_010728725.1-RS_2024_12_13", "annotation_date": "2024-12-13", "total_gene_count": "5872", "protein_coding_gene_count": "5672", "non_coding_gene_count": "54", "pubmed_id": "31287781" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2020-02-06", "dateModified": "2020-02-06", "datePublished": "2020-02-06", "_annotation": { "sample_count": 1, "sample_organism": [ "Mycobacterium branderi" ], "sample_taxid": [ "43348" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "not applicable" ], "sample_host_location_id": [], "data_size": "1.641 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "5979623", "Number of Sequences": "2", "Longest Sequences (bp)": "5115366", "N50 (bp)": "5115366", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "66.5", "Number of CDSs": "5860", "Average Protein Length": "315.3", "Coding Ratio (%)": "92.7", "Number of rRNAs": "6", "Number of tRNAs": "51", "Number of CRISPRs": "0" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Mycobacterium branderi", "strain": "strain=JCM 12687", "accession": "GCA_010728725.1", "taxid": 43348, "species_taxid": 43348, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1992, "total_fragments": 1993, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium branderi", "strain": "strain=DSM 44624", "accession": "GCA_002086575.1", "taxid": 43348, "species_taxid": 43348, "relation_to_type": "type", "validated": true, "ani": 99.9791, "matched_fragments": 1937, "total_fragments": 1993, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Mycobacterium kyorinense", "strain": "strain=DSM 45166", "accession": "GCA_002101735.1", "taxid": 487514, "species_taxid": 487514, "relation_to_type": "type", "validated": true, "ani": 90.8049, "matched_fragments": 1389, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium celatum", "strain": "strain=DSM 44243", "accession": "GCA_002101595.1", "taxid": 28045, "species_taxid": 28045, "relation_to_type": "type", "validated": true, "ani": 90.7991, "matched_fragments": 1345, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium kyorinense", "strain": "strain=KUM060204T", "accession": "GCA_000759695.1", "taxid": 487514, "species_taxid": 487514, "relation_to_type": "type", "validated": true, "ani": 90.7623, "matched_fragments": 1363, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium celatum", "strain": "strain=ATCC 51131", "accession": "GCA_000974705.1", "taxid": 28045, "species_taxid": 28045, "relation_to_type": "type", "validated": true, "ani": 90.4776, "matched_fragments": 1024, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium fragae", "strain": "strain=DSM 45731", "accession": "GCA_002102185.1", "taxid": 1260918, "species_taxid": 1260918, "relation_to_type": "type", "validated": true, "ani": 82.6439, "matched_fragments": 1129, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycobacterium noviomagense", "strain": "strain=DSM 45145", "accession": "GCA_002086415.1", "taxid": 459858, "species_taxid": 459858, "relation_to_type": "type", "validated": true, "ani": 81.68, "matched_fragments": 1041, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter kumamotonensis", "strain": "strain=DSM 45093", "accession": "GCA_002086285.1", "taxid": 354243, "species_taxid": 354243, "relation_to_type": "type", "validated": true, "ani": 80.3425, "matched_fragments": 787, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter senuensis", "strain": "strain=JCM 16017", "accession": "GCA_010723225.1", "taxid": 386913, "species_taxid": 386913, "relation_to_type": "type", "validated": true, "ani": 80.16, "matched_fragments": 815, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Mycolicibacter senuensis", "strain": "strain=DSM 44999", "accession": "GCA_002101885.1", "taxid": 386913, "species_taxid": 386913, "relation_to_type": "type", "validated": true, "ani": 80.1243, "matched_fragments": 815, "total_fragments": 1993, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_010728725.1", "gtdb_species": "s__Mycobacterium branderi", "ani": 100.0, "matched_fragments": 1992, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "conclusive" }, { "accession": "GCF_002101735.1", "gtdb_species": "s__Mycobacterium kyorinense", "ani": 90.8127, "matched_fragments": 1389, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.84", "min_intra_species_ani": "99.84", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002101595.1", "gtdb_species": "s__Mycobacterium celatum", "ani": 90.7924, "matched_fragments": 1346, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.99", "min_intra_species_ani": "99.99", "mean_intra_species_af": "0.99", "min_intra_species_af": "0.99", "num_clustered_genomes": 2, "status": "-" }, { "accession": "GCF_003402475.1", "gtdb_species": "s__Mycobacterium sp003402475", "ani": 90.1762, "matched_fragments": 1387, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001672775.1", "gtdb_species": "s__Mycobacterium kyorinense_A", "ani": 83.0517, "matched_fragments": 1110, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCA_002101905.1", "gtdb_species": "s__Mycobacterium shimoidei", "ani": 82.7316, "matched_fragments": 1061, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.72", "min_intra_species_ani": "99.46", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002102185.1", "gtdb_species": "s__Mycobacterium fragae", "ani": 82.6407, "matched_fragments": 1130, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_000277125.1", "gtdb_species": "s__Mycobacterium intracellulare", "ani": 81.0337, "matched_fragments": 993, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.48", "min_intra_species_ani": "95.71", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.84", "num_clustered_genomes": 82, "status": "-" }, { "accession": "GCF_001667945.1", "gtdb_species": "s__Mycobacterium sinense_B", "ani": 80.3401, "matched_fragments": 786, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.61", "min_intra_species_ani": "99.42", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_001667375.1", "gtdb_species": "s__Mycobacterium sinense_A", "ani": 80.2209, "matched_fragments": 806, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.51", "min_intra_species_ani": "95.04", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.89", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_002101885.1", "gtdb_species": "s__Mycobacterium senuense", "ani": 80.1258, "matched_fragments": 814, "total_fragments": 1993, "gtdb_taxonomy": "d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "100.00", "min_intra_species_ani": "100.00", "mean_intra_species_af": "1.00", "min_intra_species_af": "1.00", "num_clustered_genomes": 2, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": 0.079, "cell_length": 0.096, "doubling_h": 1.493, "growth_tmp": 37.0, "optimum_tmp": 33.654, "optimum_ph": 6.706, "genome_size": 5658460.823, "gc_content": 66.422, "coding_genes": 4941.245, "rRNA16S_genes": 1.504, "tRNA_genes": 48.184, "gram_stain": 1.0, "sporulation": 0.0, "motility": 0.0, "range_salinity": 0.2, "facultative_respiration": 0.0, "anaerobic_respiration": 0.0, "aerobic_respiration": 1.0, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 0.842, "coccus_cell_shape": 0.057, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.1, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Mycobacterium", "branderi" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }